Mutated immunoglobulin-binding polypeptides

ABSTRACT

An Fc-binding polypeptide of improved alkali stability, comprising a mutant of an Fc-binding domain of Staphylococcus Protein A (SpA), as defined by SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO:3, SEQ ID NO: 4, SEQ ID NO: 5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:22, SEQ ID NO 51 or SEQ ID NO 52 wherein at least the asparagine or serine residue at the position corresponding to position 11 in SEQ ID NO:4-7 has been mutated to an amino acid selected from the group consisting of glutamic acid, lysine, tyrosine, threonine, phenylalanine, leucine, isoleucine, tryptophan, methionine, valine, alanine, histidine and arginine.

TECHNICAL FIELD OF THE INVENTION

The present invention relates to the field of affinity chromatography,and more specifically to mutated immunoglobulin-binding domains ofProtein A, which are useful in affinity chromatography ofimmunoglobulins. The invention also relates to multimers of the mutateddomains and to separation matrices containing the mutated domains ormultimers.

BACKGROUND OF THE INVENTION

Immunoglobulins represent the most prevalent biopharmaceutical productsin either manufacture or development worldwide. The high commercialdemand for and hence value of this particular therapeutic market has ledto the emphasis being placed on pharmaceutical companies to maximize theproductivity of their respective mAb manufacturing processes whilstcontrolling the associated costs.

Affinity chromatography is used in most cases, as one of the key stepsin the purification of these immunoglobulin molecules, such asmonoclonal or polyclonal antibodies. A particularly interesting class ofaffinity reagents is proteins capable of specific binding to invariableparts of an immunoglobulin molecule, such interaction being independenton the antigen-binding specificity of the antibody. Such reagents can bewidely used for affinity chromatography recovery of immunoglobulins fromdifferent samples such as but not limited to serum or plasmapreparations or cell culture derived feed stocks. An example of such aprotein is staphylococcal protein A, containing domains capable ofbinding to the Fc and Fab portions of IgG immunoglobulins from differentspecies. These domains are commonly denoted as the E-, D-, A-, B- andC-domains.

Staphylococcal protein A (SpA) based reagents have due to their highaffinity and selectivity found a widespread use in the field ofbiotechnology, e.g. in affinity chromatography for capture andpurification of antibodies as well as for detection or quantification.At present, SpA-based affinity medium probably is the most widely usedaffinity medium for isolation of monoclonal antibodies and theirfragments from different samples including industrial cell culturesupernatants. Accordingly, various matrices comprising protein A-ligandsare commercially available, for example, in the form of native protein A(e.g. Protein A SEPHAROSE™, GE Healthcare, Uppsala, Sweden) and alsocomprised of recombinant protein A (e.g. rProtein A-SEPHAROSE™, GEHealthcare). More specifically, the genetic manipulation performed inthe commercial recombinant protein A product is aimed at facilitatingthe attachment thereof to a support and at increasing the productivityof the ligand.

These applications, like other affinity chromatography applications,require comprehensive attention to definite removal of contaminants.Such contaminants can for example be non-eluted molecules adsorbed tothe stationary phase or matrix in a chromatographic procedure, such asnon-desired biomolecules or microorganisms, including for exampleproteins, carbohydrates, lipids, bacteria and viruses. The removal ofsuch contaminants from the matrix is usually performed after a firstelution of the desired product in order to regenerate the matrix beforesubsequent use. Such removal usually involves a procedure known ascleaning-in-place (CIP), wherein agents capable of eluting contaminantsfrom the stationary phase are used. One such class of agents often usedis alkaline solutions that are passed over said stationary phase. Atpresent the most extensively used cleaning and sanitizing agent is NaOH,and the concentration thereof can range from 0.1 up to e.g. 1 M,depending on the degree and nature of contamination. This strategy isassociated with exposing the matrix to solutions with pH-values above13. For many affinity chromatography matrices containing proteinaceousaffinity ligands such alkaline environment is a very harsh condition andconsequently results in decreased capacities owing to instability of theligand to the high pH involved.

An extensive research has therefore been focused on the development ofengineered protein ligands that exhibit an improved capacity towithstand alkaline pH-values. For example, Gülich et al. (SusanneGülich, Martin Linhult, Per-Åke Nygren, Mathias Uhlén, Sophia Hober,Journal of Biotechnology 80 (2000), 169-178) suggested proteinengineering to improve the stability properties of a Streptococcalalbumin-binding domain (ABD) in alkaline environments. Gülich et al.created a mutant of ABD, wherein all the four asparagine residues havebeen replaced by leucine (one residue), aspartate (two residues) andlysine (one residue). Further, Gülich et al. report that their mutantexhibits a target protein binding behavior similar to that of the nativeprotein, and that affinity columns containing the engineered ligand showhigher binding capacities after repeated exposure to alkaline conditionsthan columns prepared using the parental non-engineered ligand. Thus, itis concluded therein that all four asparagine residues can be replacedwithout any significant effect on structure and function.

Recent work shows that changes can also be made to protein A (SpA) toeffect similar properties. US patent application publication US2005/0143566, which is hereby incorporated by reference in its entirety,discloses that when at least one asparagine residue is mutated to anamino acid other than glutamine or aspartic acid, the mutation confersan increased chemical stability at pH-values of up to about 13-14compared to the parental SpA, such as the B-domain of SpA, or Protein Z,a synthetic construct derived from the B-domain of SpA (U.S. Pat. No.5,143,844, incorporated by reference in its entirety). The authors showthat when these mutated proteins are used as affinity ligands, theseparation media as expected can better withstand cleaning proceduresusing alkaline agents. Further mutations of protein A domains with thepurpose of increasing the alkali stability have also been published inWO 2008/039141, JP 2006304633A, EP 1992692A1, EP 2202310A2, WO2010/110288, WO 2012/086660, WO 2012/083425, WO 2012/087230 and WO2014/146350, all of which are hereby incorporated by reference in theirentireties. However, the currently available mutants are still sensitiveto alkaline pH and the NaOH concentration during cleaning is usuallylimited to 0.1 M, which means that complete cleaning is difficult toachieve. Higher NaOH concentrations, which would improve the cleaning,lead to unacceptable capacity losses.

There is thus still a need in this field to obtain a separation matrixcontaining protein ligands having a further improved stability towardsalkaline cleaning procedures.

SUMMARY OF THE INVENTION

One aspect of the invention is to provide a polypeptide with improvedalkaline stability. This is achieved with a polypeptide as defined inclaim 1.

One advantage is that the alkaline stability is improved over theparental polypeptides, with a maintained highly selective bindingtowards immunoglobulins and other Fc-containing proteins.

A second aspect of the invention is to provide a multimer with improvedalkaline stability, comprising a plurality of polypeptides. This isachieved with a multimer as defined in the claims.

A third aspect of the invention is to provide a nucleic acid or a vectorencoding a polypeptide or multimer with improved alkaline stability.This is achieved with a nucleic acid or vector as defined in the claims.

A fourth aspect of the invention is to provide an expression systemcapable of expressing a polypeptide or multimer with improved alkalinestability. This is achieved with an expression system as defined in theclaims.

A fifth aspect of the invention is to provide a separation matrixcapable of selectively binding immunoglobulins and other Fc-containingproteins and exhibiting an improved alkaline stability. This is achievedwith a separation matrix as defined in the claims.

A sixth aspect of the invention is to provide an efficient andeconomical method of isolating an immunoglobulin or other Fc-containingprotein. This is achieved with a method as defined in the claims.

Further suitable embodiments of the invention are described in thedependent claims.

Definitions

The terms “antibody” and “immunoglobulin” are used interchangeablyherein, and are understood to include also fragments of antibodies,fusion proteins comprising antibodies or antibody fragments andconjugates comprising antibodies or antibody fragments.

The terms an “Fc-binding polypeptide” and “Fc-binding protein” mean apolypeptide or protein respectively, capable of binding to thecrystallisable part (Fc) of an antibody and includes e.g. Protein A andProtein G, or any fragment or fusion protein thereof that has maintainedsaid binding property.

The term “linker” herein means an element linking two polypeptide units,monomers or domains to each other in a multimer.

The term “spacer” herein means an element connecting a polypeptide or apolypeptide multimer to a support.

BRIEF DESCRIPTION OF FIGURES

FIG. 1 shows an alignment of the Fc-binding domains as defined by SEQ IDNO:1-7 and 51-52.

FIG. 2 shows results from Example 2 for the alkali stability of parentaland mutated tetrameric Zvar (SEQ ID NO 7) polypeptide variants coupledto an SPR biosensor chip.

FIG. 3 shows results from Example 4 for the alkali stability (0.5 MNaOH) of parental and mutated tetrameric Zvar (SEQ ID NO 7) polypeptidevariants coupled to agarose beads.

FIG. 4 shows results from Example 4 for the alkali stability (1.0 MNaOH) of parental and mutated tetrameric Zvar (SEQ ID NO 7) polypeptidevariants coupled to agarose beads.

DETAILED DESCRIPTION OF EMBODIMENTS

In one aspect the present invention discloses an Fc-binding polypeptide,which comprises, or consists essentially of, a mutant of an Fc-bindingdomain of Staphylococcus Protein A (SpA), as defined by, or having atleast 90%, at least 95% or at least 98% identity to, SEQ ID NO: 1(E-domain), SEQ ID NO: 2 (D-domain), SEQ ID NO:3 (A-domain), SEQ IDNO:22 (variant A-domain), SEQ ID NO: 4 (B-domain), SEQ ID NO: 5(C-domain), SEQ ID NO:6 (Protein Z) , SEQ ID NO:7 (Zvar), SEQ ID NO 51(Zvar without the linker region amino acids 1-6) or SEQ ID NO 52(C-domain without the linker region amino acids 1-6) as illustrated inFIG. 1, wherein at least the asparagine (or serine, in the case of SEQID NO 2) residue at the position* corresponding to position 11 in SEQ IDNO:4-7 has been mutated to an amino acid selected from the groupconsisting of glutamic acid, lysine, tyrosine, threonine, phenylalanine,leucine, isoleucine, tryptophan, methionine, valine, alanine, histidineand arginine. Protein Z (SEQ ID NO:6) is a mutated B-domain as disclosedin U.S. Pat. No. 5,143,844, while SEQ ID NO 7 denotes a further mutatedvariant of Protein Z, here called Zvar, with the mutations N3A,N6D,N23T.SEQ ID NO:22 is a natural variant of the A-domain in Protein A fromStaphylococcus aureus strain N315, having an A46S mutation, using theposition terminology of FIG. 1. The mutation of N11 in these domainsconfers an improved alkali stability in comparison with the parentaldomain/polypeptide, without impairing the immunoglobulin-bindingproperties. Hence, the polypeptide can also be described as an Fc- orimmunoglobulin-binding polypeptide, or alternatively as an Fc- orimmunoglobulin-binding polypeptide unit. *Throughout this description,the amino acid residue position numbering convention of FIG. 1 is used,and the position numbers are designated as corresponding to those in SEQID NO 4-7.

In alternative language, the invention discloses an Fc-bindingpolypeptide which comprises a sequence as defined by, or having at least90%, at least 95% or at least 98% identity to SEQ ID NO 53.

SEQ ID NO 53 KEX₁Q X₂AFYEILX₃LP NLTEEQRX₄X₅F IX₆X₇LKDX₈PSX₉SX₁₀X₁₁X₁₂LAEAKX₁₃ X₁₄NDAQAPK

where individually of each other:

X₁=A or Q

X₂=E,K,Y,T,F,L,W,I,M,V,A,H or R

X₃=H or K

X₄=A or N

X₅=A or G

X₆=Q or E

X₇=S or K

X₈=E or D

X₉=Q or V

X₁₀=K,R or A

X₁₁=A,E or N

X₁₂=I or L

X₁₃=K or R

X₁₄=L or Y

The N11 (X₂) mutation (e.g. a N11E or N11K mutation) may be the onlymutation or the polypeptide may also comprise further mutations, such assubstitutions in at least one of the positions corresponding topositions 3, 6, 9, 10, 15, 18, 23, 28, 29, 32, 33, 36, 37, 40, 42, 43,44, 47, 50, 51, 55 and 57 in SEQ ID NO:4-7. In one or more of thesepositions, the original amino acid residue may e.g. be substituted withan amino acid which is not asparagine, proline or cysteine. The originalamino acid residue may e.g. be substituted with an alanine, a valine, athreonine, a serine, a lysine, a glutamic acid or an aspartic acid.Further, one or more amino acid residues may be deleted, e.g. frompositions 1-6 and/or from positions 56-58.

In some embodiments, the amino acid residue at the positioncorresponding to position 9 in SEQ ID NO:4-7 (X₁) is an amino acid otherthan glutamine, asparagine, proline or cysteine, such as an alanine. Thecombination of the mutations at positions 9 and 11 provides particularlygood alkali stability, as shown by the examples. In specificembodiments, in SEQ ID NO: 7 the amino acid residue at position 9 is analanine and the amino acid residue at position 11 is a lysine orglutamic acid, such as a lysine. Mutations at position 9 are alsodiscussed in copending application PCT/SE2014/050872, which is herebyincorporated by reference in its entirety.

In some embodiments, the amino acid residue at the positioncorresponding to position 50 in SEQ ID NO:4-7 (X₁₃) is an arginine or aglutamic acid.

In certain embodiments, the amino acid residue at the positioncorresponding to position 3 in SEQ ID NO:4-7 is an alanine and/or theamino acid residue at the position corresponding to position 6 in SEQ IDNO:4-7 is an aspartic acid. One of the amino acid residues at positions3 and 6 may be an asparagine and in an alternative embodiment both aminoacid residues at positions 3 and 6 may be asparagines.

In some embodiments the amino acid residue at the position correspondingto position 43 in SEQ ID NO:4-7 (X₁₁) is an alanine or a glutamic acid,such as an alanine. In specific embodiments, the amino acid residues atpositions 9 and 11 in SEQ ID NO: 7 are alanine and lysine/glutamic acidrespectively, while the amino acid residue at position 43 is alanine orglutamic acid.

In certain embodiments the amino acid residue residue at the positioncorresponding to position 28 in SEQ ID NO:4-7 (X₅) is an alanine or anasparagine, such as an alanine.

In some embodiments the amino acid residue at the position correspondingto position 40 in SEQ ID NO:4-7 (X₉) is selected from the groupconsisting of asparagine, alanine, glutamic acid and valine, or from thegroup consisting of glutamic acid and valine. In specific embodiments,the amino acid residues at positions 9 and 11 in SEQ ID NO: 7 arealanine and glutamic acid respectively, while the amino acid residue atposition 40 is valine. Optionally, the amino acid residue at position 43may then be alanine or glutamic acid.

In certain embodiments, the amino acid residue at the positioncorresponding to position 42 in SEQ ID NO:4-7 (X₁₀) is an alanine,lysine or arginine.

In some embodiments the amino acid residue at the position correspondingto position 18 in SEQ ID NO:4-7 (X₃) is a lysine or a histidine, such asa lysine.

In certain embodiments the amino acid residue at the positioncorresponding to position 33 in SEQ ID NO:4-7 (X₇) is a lysine or aserine, such as a lysine.

In some embodiments the amino acid residue at the position correspondingto position 37 in SEQ ID NO:4-7 (X₈) is a glutamic acid or an asparticacid, such as a glutamic acid.

In certain embodiments the amino acid residue at the positioncorresponding to position 51 in SEQ ID NO:4-7 (X₁₄) is a tyrosine or aleucine, such as a tyrosine.

In some embodiments, the amino acid residue at the positioncorresponding to position 44 in SEQ ID NO:4-7 (X₁₂) is a leucine or anisoleucine. In specific embodiments, the amino acid residues atpositions 9 and 11 in SEQ ID NO: 7 are alanine and lysine/glutamic acidrespectively, while the amino acid residue at position 44 is isoleucine.Optionally, the amino acid residue at position 43 may then be alanine orglutamic acid.

In some embodiments, the amino acid residues at the positionscorresponding to positions 1, 2, 3 and 4 or to positions 3, 4, 5 and 6in SEQ ID NO: 4-7 have been deleted. In specific variants of theseembodiments, the parental polypeptide is the C domain of Protein A (SEQID NO: 5). The effects of these deletions on the native C domain aredescribed in U.S. Pat. Nos. 9,018,305, and 8,329,860, which are herebyincorporated by reference in their entireties.

In certain embodiments, the mutation in SEQ ID NO 4-7, such as in SEQ IDNO 7, is selected from the group consisting of: N11K; N11E; N11Y; N11T;N11F; N11L; N11W; N11I; N11M; N11V; N11A; N11H; N11R; N11E,Q32A;N11E,Q32E,Q40E; N11E,Q32E,K50R; Q9A,N11E,N43A; Q9A,N11E,N28A,N43A;Q9A,N11E,Q40V,A42K,N43E,L44I; Q9A,N11E,Q40V,A42K,N43A,L44I;N11K,H18K,S33K,D37E,A42R,N43A,L44I,K50R,L51Y;Q9A,N11E,N28A,Q40V,A42K,N43A,L44I;Q9A,N11K,H18K,S33K,D37E,A42R,N43A,L44I,K50R,L51Y; N11K, H18K, D37E,A42R, N43A, L44I; Q9A, N11K, H18K, D37E, A42R, N43A, L44I; Q9A, N11K,H18K, D37E, A42R, N43A, L44I, K50R; Q9A,N11K,H18K,D37E,A42R;Q9A,N11E,D37E,Q40V,A42K,N43A,L44I and Q9A,N11E,D37E,Q40V,A42R,N43A,L44I.These mutations provide particularly high alkaline stabilities. Themutation in SEQ ID NO 4-7, such as in SEQ ID NO 7, can also be selectedfrom the group consisting of N11K; N11Y; N11F; N11L; N11W; N11I; N11M;N11V; N11A; N11H; N11R; Q9A,N11E,N43A; Q9A,N11E,N28A,N43A;Q9A,N11E,Q40V,A42K,N43E,L44I; Q9A,N11E,Q40V,A42K,N43A,L44I;Q9A,N11E,N28A,Q40V,A42K,N43A,L44I;N11K,H18K,S33K,D37E,A42R,N43A,L44I,K50R,L51Y;Q9A,N11K,H18K,S33K,D37E,A42R,N43A,L44I,K50R,L51Y; N11K, H18K, D37E,A42R, N43A, L44I; Q9A, N11K, H18K, D37E, A42R, N43A, L44I and Q9A, N11K,H18K, D37E, A42R, N43A, L44I, K50R.

In some embodiments, the polypeptide comprises or consists essentiallyof a sequence selected from the group consisting of: SEQ ID NO 8, SEQ IDNO 9, SEQ ID NO 10, SEQ ID NO 11, SEQ ID NO 12, SEQ ID NO 13, SEQ ID NO14, SEQ ID NO 15, SEQ ID NO 16, SEQ ID NO 23, SEQ ID NO 24, SEQ ID NO25, SEQ ID NO 26, SEQ ID NO 27, SEQ ID NO 28, SEQ ID NO 29, SEQ ID NO36, SEQ ID NO 37, SEQ ID NO 38, SEQ ID NO 39, SEQ ID NO 40, SEQ ID NO41, SEQ ID NO 42, SEQ ID NO 43, SEQ ID NO 44, SEQ ID NO 45, SEQ ID NO46, SEQ ID NO 47, SEQ ID NO 48, SEQ ID NO 49 and SEQ ID NO 50. It maye.g. comprise or consist essentially of a sequence selected from thegroup consisting of: SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10, SEQ ID NO11, SEQ ID NO 16, SEQ ID NO 23, SEQ ID NO 24, SEQ ID NO 25, SEQ ID NO26, SEQ ID NO 27, SEQ ID NO 28 and SEQ ID NO 29. It can also comprise orconsist essentially of a sequence selected from the group consisting of:SEQ ID NO 8, SEQ ID NO 9, SEQ ID NO 10, SEQ ID NO 11, SEQ ID NO 16, SEQID NO 23, SEQ ID NO 24, SEQ ID NO 25, SEQ ID NO 27, SEQ ID NO 28, SEQ IDNO 38, SEQ ID NO 40; SEQ ID NO 41; SEQ ID NO 42; SEQ NO 43, SEQ ID NO44, SEQ ID NO 45, SEQ ID NO 46, SEQ ID NO 47 and SEQ ID NO 48. Thepolypeptide may e.g. be defined by a sequence selected from the groupsabove or from subsets of these groups, but it may also compriseadditional amino acid residues at the N- and/or C-terminal end, e.g. aleader sequence at the N-terminal end and/or a tail sequence at theC-terminal end.

Zvar(Q9A, N11E, N43A) SEQ ID NO 8VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKZvar(Q9A, N11E, N28A, N43A) SEQ ID NO 9VDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKZvar(Q9A, N11E, Q40V, A42K, N43E, L441) SEQ ID NO 10VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKEILAEAKK LNDAQAPKZvar(Q9A, N11E, Q40V,A42K, N43A, L441) SEQ ID NO 11VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKZvar(N11E, Q32A) SEQ ID NO 12VDAKFDKEQQ EAFYEILHLP NLTEEQRNAF IASLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11E) SEQ ID NO 13VDAKFDKEQQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11E, Q32E, Q40E) SEQ ID NO 14VDAKFDKEQQ EAFYEILHLP NLTEEQRNAF IESLKDDPSE SANLLAEAKK LNDAQAPKZvar(N11E, Q32E, K50R) SEQ ID NO 15VDAKFDKEQQ EAFYEILHLP NLTEEQRNAF IESLKDDPSQ SANLLAEAKR LNDAQAPKZvar(N11K) SEQ ID NO 16VDAKFDKEQQ KAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11K, H18K, S33K, D37E, A42R, N43A, L441, K50R,L51Y) SEQ ID NO 23VDAKFDKEQQ KAFYEILKLP NLTEEQRNAF IQKLKDEPSQ SRAILAEAKR YNDAQAPKZvar(Q9A, N11E, N28A, Q40V, A42K, N43A, L441) SEQ ID NO 24VDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSV SKAILAEAKK LNDAQAPKZvar(Q9A, N11K, H18K, 533K, D37E, A42R, N43A, L441, K50R, L51Y)SEQ ID NO 25VDAKFDKEAQ KAFYEILKLP NLTEEQRAAF IQKLKDEPSQ SRAILAEAKR YNDAQAPKZvar(N11K, H18K, D37E, A42R, N43A, L44I) SEQ ID NO 26VDAKFDKEQQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRAILAEAKK LNDAQAPKZvar(Q9A, N11K, H18K, D37E, A42R, N43A, L44I) SEQ ID NO 27VDAKFDKEAQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRAILAEAKK LNDAQAPKZvar(Q9A, N11K, H18K, D37E, A42R, N43A, L44I, K50R) SEQ ID NO 28VDAKFDKEAQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRAILAEAKR LNDAQAPKZvar(Q9A, N11K, H18K, D37E, A42R) SEQ ID NO 29VDAKFDKEAQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRNLLAEAKK LNDAQAPKB(Q9A, N11E, Q40V, A42K, N43A, L44I) SEQ ID NO 36ADNKFNKEAQ EAFYEILHLP NLNEEQRNGF IQSLKDDPSV SKAILAEAKK LNDAQAPKC(Q9A, N11E, E43A) SEQ ID NO 37ADNKFNKEAQ EAFYEILHLP NLTEEQRNGF IQSLKDDPSV SKAILAEAKK LNDAQAPKZvar(N11Y) SEQ ID NO 38VDAKFDKEQQ YAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11T) SEQ ID NO 39VDAKFDKEQQ TAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11F) SEQ ID NO 40VDAKFDKEQQ FAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11L) SEQ ID NO 41VDAKFDKEQQ LAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11W) SEQ ID NO 42VDAKFDKEQQ WAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11I) SEQ ID NO 43VDAKFDKEQQ IAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11M) SEQ ID NO 44VDAKFDKEQQ MAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11V) SEQ ID NO 45VDAKFDKEQQ VAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11A) SEQ ID NO 46VDAKFDKEQQ AAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11H) SEQ ID NO 47VDAKFDKEQQ HAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(N11R) SEQ ID NO 48VDAKFDKEQQ RAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SANLLAEAKK LNDAQAPKZvar(Q9A, N11E ,D37E, Q40V, A42K, N43A, L44I) SEQ ID NO 49VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SKAILAEAKK LNDAQAPKZvar(Q9A, N11E, D37E, Q40V, A42R, N43A, L44I) SEQ ID NO 50VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SRAILAEAKK LNDAQAPK

In a second aspect the present invention discloses a multimercomprising, or consisting essentially of, a plurality of polypeptideunits as defined by any embodiment disclosed above. The multimer cane.g. be a dimer, a trimer, a tetramer, a pentamer, a hexamer, aheptamer, an octamer or a nonamer. It can be a homomultimer, where allthe units in the multimer are identical or it can be a heteromultimer,where at least one unit differs from the others. Advantageously, all theunits in the multimer are alkali stable, such as by comprising themutations disclosed above. The polypeptides can be linked to each otherdirectly by peptide bonds between the C-terminal and N-terminal ends ofthe polypeptides. Alternatively, two or more units in the multimer canbe linked by linkers comprising oligomeric or polymeric species, such aselements comprising up to 15 or 30 amino acids, such as 1-5, 1-10 or5-10 amino acids. This is the case in particular for mutations of SEQ IDNO 51 and 52 and for the SEQ ID NO 53 polypeptide, where specificexamples of linkers can e.g. be VDAKFD or ADNKFN, such as VDAKFD. Thenature of such a linker should preferably not destabilize the spatialconformation of the protein units. This can e.g. be achieved by avoidingthe presence of proline in the linkers. Furthermore, said linker shouldpreferably also be sufficiently stable in alkaline environments not toimpair the properties of the mutated protein units. For this purpose, itis advantageous if the linkers do not contain asparagine. It canadditionally be advantageous if the linkers do not contain glutamine.The multimer may further at the N-terminal end comprise a plurality ofamino acid residues e.g. originating from the cloning process orconstituting a residue from a cleaved off signaling sequence. The numberof additional amino acid residues may e.g. be 15 or less, such as 10 orless or 5 or less. As a specific example, the multimer may comprise anAQ sequence at the N-terminal end.

In certain embodiments, the multimer may comprise, or consistessentially, of a sequence selected from the group consisting of: SEQ IDNO 17, SEQ ID NO 18, SEQ ID NO 19, SEQ ID NO 20, SEQ ID NO 30, SEQ ID NO31, SEQ ID NO 32, SEQ ID NO 33, SEQ ID NO 34 and SEQ ID NO 35. Thesesequences are listed below and named as Parent(Mutations)n, where n isthe number of monomer units in a multimer.

Zvar(Q9A, N11E, N43A)4 SEQ ID NO 17AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKCZvar(Q9A, N11E, N28A, N43A)4 SEQ ID NO 18AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSQ SAALLAEAKK LNDAQAPKCZvar(Q9A, N11E, Q40V, A42K,N 43E, L441)4 SEQ ID NO 19AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKEILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKEILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKEILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKEILAEAKK LNDAQAPKCZvar(Q9A, N11E, Q40V, A42K, N43A, L441)4 SEQ ID NO 20AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKCZvar(N11K, H18K ,533K ,D37E, A42R, N43A, L441, K50R, L51Y)4 SEQ ID NO 30AQGT VDAKFDKEQQ KAFYEILKLP NLTEEQRNAF IQKLKDEPSQ SRAILAEAKR YNDAQAPKVDAKFDKEQQ KAFYEILKLP NLTEEQRNAF IQKLKDEPSQ SRAILAEAKR YNDAQAPKVDAKFDKEQQ KAFYEILKLP NLTEEQRNAF IQKLKDEPSQ SRAILAEAKR YNDAQAPKVDAKFDKEQQ KAFYEILKLP NLTEEQRNAF IQKLKDEPSQ SRAILAEAKR YNDAQAPKCZvar(Q9A, N11K, H18K, D37E, A42R)4 SEQ ID NO 31AQGT VDAKFDKEAQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRNLLAEAKK LNDAQAPKVDAKFDKEAQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRNLLAEAKK LNDAQAPKVDAKFDKEAQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRNLLAEAKK LNDAQAPKVDAKFDKEAQ KAFYEILKLP NLTEEQRNAF IQSLKDEPSQ SRNLLAEAKK LNDAQAPKCZvar(Q9A, N11E, N28A, Q40V,A42K, N43A, L441)4 SEQ ID NO 32AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRAAF IQSLKDDPSV SKAILAEAKK LNDAQAPKCZvar(Q9A, N11E, Q40V, A42K, N43A, L441)6 SEQ ID NO 33AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDDPSV SKAILAEAKK LNDAQAPKCZvar(Q9A, N11E, D37E, Q40V, A42K, N43A, L441)4 SEQ ID NO 34AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SKAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SKAILAEAKK LNDAQAPKCZvar(Q9A, N11E, D37E, Q40V, A42R, N43A, L441)4 SEQ ID NO 35AQGT VDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SRAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SRAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SRAILAEAKK LNDAQAPKVDAKFDKEAQ EAFYEILHLP NLTEEQRNAF IQSLKDEPSV SRAILAEAKK LNDAQAPKC

In some embodiments, the polypeptide and/or multimer, as disclosedabove, further comprises at the C-terminal or N-terminal end one or morecoupling elements, selected from the group consisting of one or morecysteine residues, a plurality of lysine residues and a plurality ofhistidine residues. The coupling element(s) may also be located within1-5 amino acid residues, such as within 1-3 or 1-2 amino acid residuesfrom the C-terminal or N-terminal end. The coupling element may e.g. bea single cysteine at the C-terminal end. The coupling element(s) may bedirectly linked to the C- or N-terminal end, or it/they may be linkedvia a stretch comprising up to 15 amino acids, such as 1-5, 1-10 or 5-10amino acids. This stretch should preferably also be sufficiently stablein alkaline environments not to impair the properties of the mutatedprotein. For this purpose, it is advantageous if the stretch does notcontain asparagine. It can additionally be advantageous if the stretchdoes not contain glutamine. An advantage of having a C-terminal cysteineis that endpoint coupling of the protein can be achieved throughreaction of the cysteine thiol with an electrophilic group on a support.This provides excellent mobility of the coupled protein which isimportant for the binding capacity.

The alkali stability of the polypeptide or multimer can be assessed bycoupling it to an SPR chip, e.g. to Biacore CM5 sensor chips asdescribed in the examples, using e.g. NHS— or maleimide couplingchemistries, and measuring the immunoglobulin-binding capacity of thechip, typically using polyclonal human IgG, before and after incubationin alkaline solutions at a specified temperature, e.g. 22+/−2° C. Theincubation can e.g. be performed in 0.5 M NaOH for a number of 10 mincycles, such as 100, 200 or 300 cycles. The IgG capacity of the matrixafter 100 10 min incubation cycles in 0.5 M NaOH at 22+/−2° C. can be atleast 55, such as at least 60, at least 80 or at least 90% of the IgGcapacity before the incubation. Alternatively, the remaining IgGcapacity after 100 cycles for a particular mutant measured as above canbe compared with the remaining IgG capacity for the parentalpolypeptide/multimer. In this case, the remaining IgG capacity for themutant may be at least 105%, such as at least 110%, at least 125%, atleast 150% or at least 200% of the parental polypeptide/multimer.

In a third aspect the present invention discloses a nucleic acidencoding a polypeptide or multimer according to any embodiment disclosedabove. Thus, the invention encompasses all forms of the present nucleicacid sequence such as the RNA and the DNA encoding the polypeptide ormultimer. The invention embraces a vector, such as a plasmid, which inaddition to the coding sequence comprises the required signal sequencesfor expression of the polypeptide or multimer according the invention.In one embodiment, the vector comprises nucleic acid encoding a multimeraccording to the invention, wherein the separate nucleic acids encodingeach unit may have homologous or heterologous DNA sequences.

In a fourth aspect the present invention discloses an expression system,which comprises, a nucleic acid or a vector as disclosed above. Theexpression system may e.g. be a gram-positive or gram-negativeprokaryotic host cell system, e.g. E. coli or Bacillus sp. which hasbeen modified to express the present polypeptide or multimer. In analternative embodiment, the expression system is a eukaryotic host cellsystem, such as a yeast, e.g. Pichia pastoris or Saccharomycescerevisiae, or mammalian cells, e.g. CHO cells.

In a fifth aspect, the present invention discloses a separation matrix,wherein a plurality of polypeptides or multimers according to anyembodiment disclosed above have been coupled to a solid support. Such amatrix is useful for separation of immunoglobulins or otherFc-containing proteins and, due to the improved alkali stability of thepolypeptides/multimers, the matrix will withstand highly alkalineconditions during cleaning, which is essential for long-term repeateduse in a bioprocess separation setting. The alkali stability of thematrix can be assessed by measuring the immunoglobulin-binding capacity,typically using polyclonal human IgG, before and after incubation inalkaline solutions at a specified temperature, e.g. 22+/−2° C. Theincubation can e.g. be performed in 0.5 M or 1.0 M NaOH for a number of15 min cycles, such as 100, 200 or 300 cycles, corresponding to a totalincubation time of 25, 50 or 75 h. The IgG capacity of the matrix after96-100 15 min incubation cycles or a total incubation time of 24 or 25 hin 0.5 M NaOH at 22+/−2° C. can be at least 80, such as at least 85, atleast 90 or at least 95% of the IgG capacity before the incubation. Thecapacity of the matrix after a total incubation time of 24 h in 1.0 MNaOH at 22+/−2° C. can be at least 70, such as at least 80 or at least90% of the IgG capacity before the incubation.

As the skilled person will understand, the expressed polypeptide ormultimer should be purified to an appropriate extent before beingimmobilized to a support. Such purification methods are well known inthe field, and the immobilization of protein-based ligands to supportsis easily carried out using standard methods. Suitable methods andsupports will be discussed below in more detail.

The solid support of the matrix according to the invention can be of anysuitable well-known kind. A conventional affinity separation matrix isoften of organic nature and based on polymers that expose a hydrophilicsurface to the aqueous media used, i.e. expose hydroxy (—OH), carboxy(—COOH), carboxamido (—CONH₂, possibly in N-substituted forms), amino(—NH₂, possibly in substituted form), oligo- or polyethylenoxy groups ontheir external and, if present, also on internal surfaces. The solidsupport can suitably be porous. The porosity can be expressed as a Kayor Kd value (the fraction of the pore volume available to a probemolecule of a particular size) measured by inverse size exclusionchromatography, e.g. according to the methods described in GelFiltration Principles and Methods, Pharmacia LKB Biotechnology 1991, pp6-13. By definition, both Kd and Kay values always lie within the range0-1. The Kay value can advantageously be 0.6-0.95, e.g. 0.7-0.90 or0.6-0.8, as measured with dextran of Mw 110 kDa as a probe molecule. Anadvantage of this is that the support has a large fraction of pores ableto accommodate both the polypeptides/multimers of the invention andimmunoglobulins binding to the polypeptides/multimers and to providemass transport of the immunoglobulins to and from the binding sites.

The polypeptides or multimers may be attached to the support viaconventional coupling techniques utilising e.g. thiol, amino and/orcarboxy groups present in the ligand. Bisepoxides, epichlorohydrin,CNBr, N-hydroxysuccinimide (NHS) etc are well-known coupling reagents.Between the support and the polypeptide/multimer, a molecule known as aspacer can be introduced, which improves the availability of thepolypeptide/multimer and facilitates the chemical coupling of thepolypeptide/multimer to the support. Depending on the nature of thepolypeptide/multimer and the coupling conditions, the coupling may be amultipoint coupling (e.g. via a plurality of lysines) or a single pointcoupling (e.g. via a single cysteine). Alternatively, thepolypeptide/multimer may be attached to the support by non-covalentbonding, such as physical adsorption or biospecific adsorption.

In some embodiments the matrix comprises 5-25, such as 5-20 mg/ml, 5-15mg/ml, 5-11 mg/ml or 6-11 mg/ml of the polypeptide or multimer coupledto the support. The amount of coupled polypeptide/multimer can becontrolled by the concentration of polypeptide/multimer used in thecoupling process, by the activation and coupling conditions used and/orby the pore structure of the support used. As a general rule theabsolute binding capacity of the matrix increases with the amount ofcoupled polypeptide/multimer, at least up to a point where the poresbecome significantly constricted by the coupled polypeptide/multimer.The relative binding capacity per mg coupled polypeptide/multimer willdecrease at high coupling levels, resulting in a cost-benefit optimumwithin the ranges specified above.

In certain embodiments the polypeptides or multimers are coupled to thesupport via thioether bonds. Methods for performing such coupling arewell-known in this field and easily performed by the skilled person inthis field using standard techniques and equipment. Thioether bonds areflexible and stable and generally suited for use in affinitychromatography. In particular when the thioether bond is via a terminalor near-terminal cysteine residue on the polypeptide or multimer, themobility of the coupled polypeptide/multimer is enhanced which providesimproved binding capacity and binding kinetics. In some embodiments thepolypeptide/multimer is coupled via a C-terminal cysteine provided onthe protein as described above. This allows for efficient coupling ofthe cysteine thiol to electrophilic groups, e.g. epoxide groups,halohydrin groups etc. on a support, resulting in a thioether bridgecoupling.

In certain embodiments the support comprises a polyhydroxy polymer, suchas a polysaccharide. Examples of polysaccharides include e.g. dextran,starch, cellulose, pullulan, agar, agarose etc. Polysaccharides areinherently hydrophilic with low degrees of nonspecific interactions,they provide a high content of reactive (activatable) hydroxyl groupsand they are generally stable towards alkaline cleaning solutions usedin bioprocessing.

In some embodiments the support comprises agar or agarose. The supportsused in the present invention can easily be prepared according tostandard methods, such as inverse suspension gelation (S Hjertén:Biochim Biophys Acta 79(2), 393-398 (1964). Alternatively, the basematrices are commercially available products, such as crosslinkedagarose beads sold under the name of SEPHAROSE™ FF (GE Healthcare). Inan embodiment, which is especially advantageous for large-scaleseparations, the support has been adapted to increase its rigidity usingthe methods described in U.S. Pat. No. 6,602,990 or U.S. Pat. No.7,396,467, which are hereby incorporated by reference in their entirety,and hence renders the matrix more suitable for high flow rates.

In certain embodiments the support, such as a polysaccharide or agarosesupport, is crosslinked, such as with hydroxyalkyl ether crosslinks.Crosslinker reagents producing such crosslinks can be e.g.epihalohydrins like epichlorohydrin, diepoxides like butanedioldiglycidyl ether, allylating reagents like allyl halides or allylglycidyl ether. Crosslinking is beneficial for the rigidity of thesupport and improves the chemical stability. Hydroxyalkyl ethercrosslinks are alkali stable and do not cause significant nonspecificadsorption.

Alternatively, the solid support is based on synthetic polymers, such aspolyvinyl alcohol, polyhydroxyalkyl acrylates, polyhydroxyalkylmethacrylates, polyacrylamides, polymethacrylamides etc. In case ofhydrophobic polymers, such as matrices based on divinyl andmonovinyl-substituted benzenes, the surface of the matrix is oftenhydrophilised to expose hydrophilic groups as defined above to asurrounding aqueous liquid. Such polymers are easily produced accordingto standard methods, see e.g. “Styrene based polymer supports developedby suspension polymerization” (R Arshady: Chimica e L'Industria 70(9),70-75 (1988)). Alternatively, a commercially available product, such asSOURCE™ (GE Healthcare) is used. In another alternative, the solidsupport according to the invention comprises a support of inorganicnature, e.g. silica, zirconium oxide etc.

In yet another embodiment, the solid support is in another form such asa surface, a chip, capillaries, or a filter (e.g. a membrane or a depthfilter matrix).

As regards the shape of the matrix according to the invention, in oneembodiment the matrix is in the form of a porous monolith. In analternative embodiment, the matrix is in beaded or particle form thatcan be porous or non-porous. Matrices in beaded or particle form can beused as a packed bed or in a suspended form. Suspended forms includethose known as expanded beds and pure suspensions, in which theparticles or beads are free to move. In case of monoliths, packed bedand expanded beds, the separation procedure commonly followsconventional chromatography with a concentration gradient. In case ofpure suspension, batch-wise mode will be used.

In a sixth aspect, the present invention discloses a method of isolatingan immunoglobulin, wherein a separation matrix as disclosed above isused.

In certain embodiments, the method comprises the steps of:

a) contacting a liquid sample comprising an immunoglobulin with aseparation matrix as disclosed above,

b) washing said separation matrix with a washing liquid,

c) eluting the immunoglobulin from the separation matrix with an elutionliquid, and

d) cleaning the separation matrix with a cleaning liquid, which canalternatively be called a cleaning-in-place (CIP) liquid, e.g. with acontact (incubation) time of at least 10 min.

The method may also comprise steps of, before step a), providing anaffinity separation matrix according to any of the embodiments describedabove and providing a solution comprising an immunoglobulin and at leastone other substance as a liquid sample and of, after step c), recoveringthe eluate and optionally subjecting the eluate to further separationsteps, e.g. by anion or cation exchange chromatography, multimodalchromatography and/or hydrophobic interaction chromatography. Suitablecompositions of the liquid sample, the washing liquid and the elutionliquid, as well as the general conditions for performing the separationare well known in the art of affinity chromatography and in particularin the art of Protein A chromatography. The liquid sample comprising anFc-containing protein and at least one other substance may comprise hostcell proteins (HCP), such as CHO cell, E. coli or yeast proteins.Contents of CHO cell and E. coli proteins can conveniently be determinedby immunoassays directed towards these proteins, e.g. the CHO HCP or E.coli HCP ELISA kits from Cygnus Technologies. The host cell proteins orCHO cell/E. coli proteins may be desorbed during step b).

The elution may be performed by using any suitable solution used forelution from Protein A media. This can e.g. be a solution or buffer withpH 5 or lower, such as pH 2.5-5 or 3-5. It can also in some cases be asolution or buffer with pH 11 or higher, such as pH 11-14 or pH 11-13.In some embodiments the elution buffer or the elution buffer gradientcomprises at least one mono- di- or trifunctional carboxylic acid orsalt of such a carboxylic acid. In certain embodiments the elutionbuffer or the elution buffer gradient comprises at least one anionspecies selected from the group consisting of acetate, citrate, glycine,succinate, phosphate, and formiate.

In some embodiments, the cleaning liquid is alkaline, such as with a pHof 13-14. Such solutions provide efficient cleaning of the matrix, inparticular at the upper end of the interval

In certain embodiments, the cleaning liquid comprises 0.1-2.0 M NaOH orKOH, such as 0.5-2.0 or 0.5-1.0 M NaOH or KOH. These are efficientcleaning solutions, and in particular so when the NaOH or KOHconcentration is above 0.1 M or at least 0.5 M. The high stability ofthe polypeptides of the invention enables the use of such stronglyalkaline solutions.

The method may also include a step of sanitizing the matrix with asanitization liquid, which may e.g. comprise a peroxide, such ashydrogen peroxide and/or a peracid, such as peracetic acid or performicacid.

In some embodiments, steps a)-d) are repeated at least 10 times, such asat least 50 times, 50-200, 50-300 or 50-500 times. This is important forthe process economy in that the matrix can be re-used many times.

Steps a)-c) can also be repeated at least 10 times, such as at least 50times, 50-200, 50-300 or 50-500 times, with step d) being performedafter a plurality of instances of step c), such that step d) isperformed at least 10 times, such as at least 50 times. Step d) can e.g.be performed every second to twentieth instance of step c).

EXAMPLES Mutagenesis of Protein

Site-directed mutagenesis was performed by a two-step PCR usingoligonucleotides coding for the mutations. As template a plasmidcontaining a single domain of either Z, B or C was used. The PCRfragments were ligated into an E. coli expression vector. DNA sequencingwas used to verify the correct sequence of inserted fragments.

To form multimers of mutants an Acc I site located in the startingcodons (GTA GAC) of the B, C or Z domain was used, corresponding toamino acids VD. The vector for the monomeric domain was digested withAcc I and phosphatase treated. Acc I sticky-ends primers were designed,specific for each variant, and two overlapping PCR products weregenerated from each template. The PCR products were purified and theconcentration was estimated by comparing the PCR products on a 2%agarose gel. Equal amounts of the pair wise PCR products were hybridized(90° C.->25° C. in 45 min) in ligation buffer. The resulting productconsists approximately to ¼ of fragments likely to be ligated into anAcc I site (correct PCR fragments and/or the digested vector). Afterligation and transformation colonies were PCR screened to identifyconstructs containing the desired mutant. Positive clones were verifiedby DNA sequencing.

Construct Expression and Purification

The constructs were expressed in the bacterial periplasm by fermentationof E. coli K12 in standard media. After fermentation the cells wereheat-treated to release the periplasm content into the media. Theconstructs released into the medium were recovered by microfiltrationwith a membrane having a 0.2 μm pore size.

Each construct, now in the permeate from the filtration step, waspurified by affinity. The permeate was loaded onto a chromatographymedium containing immobilized IgG (IgG Sepharose 6FF, GE Healthcare).The loaded product was washed with phosphate buffered saline and elutedby lowering the pH.

The elution pool was adjusted to a neutral pH (pH 8) and reduced byaddition of dithiothreitol. The sample was then loaded onto an anionexchanger. After a wash step the construct was eluted in a NaCl gradientto separate it from any contaminants. The elution pool was concentratedby ultrafiltration to 40-50 mg/ml. It should be noted that thesuccessful affinity purification of a construct on an immobilized IgGmedium indicates that the construct in question has a high affinity toIgG.

The purified ligands were analyzed with RPC LC-MS to determine thepurity and to ascertain that the molecular weight corresponded to theexpected (based on the amino acid sequence).

Example 1

The purified monomeric ligands listed in Table 1, further comprising anAQGT leader sequence at the N-terminus and a cysteine at the C terminus,were immobilized on Biacore CM5 sensor chips (GE Healthcare, Sweden),using the amine coupling kit of GE Healthcare (for carbodiimide couplingof amines on the carboxymethyl groups on the chip) in an amountsufficient to give a signal strength of about 200-1500 RU in a Biacoresurface plasmon resonance (SPR) instrument (GE Healthcare, Sweden) . Tofollow the IgG binding capacity of the immobilized surface 1 mg/ml humanpolyclonal IgG (Gammanorm) was flowed over the chip and the signalstrength (proportional to the amount of binding) was noted. The surfacewas then cleaned-in-place (CIP), i.e. flushed with 500 mM NaOH for 10minutes at room temperature (22+/−2° C.). This was repeated for 96-100cycles and the immobilized ligand alkaline stability was followed as theremaining IgG binding capacity (signal strength) after each cycle. Theresults are shown in Table 1 and indicate that at least the ligandsZvar(N11K)1, Zvar(N11E)1, Zvar(N11Y)1, Zvar(N11T)1, Zvar(N11F)1,Zvar(N11L)1, Zvar(N11W)1, ZN11I)1, Zvar(N11M)1, Zvar(N11V)1,Zvar(N11A)1, Zvar(N11H1), Zvar(N11R)1, Zvar(N11E,Q32A)1,Zvar(N11E,Q32E,Q40E)1 and Zvar(N11E,Q32E,K50R)1, Zvar(Q9A,N11E,N43A)1,Zvar(Q9A,N11E,N28A,N43A)1, Zvar(Q9A,N11E,Q40V,A42K,N43E,L44I)1,Zvar(Q9A,N11E,Q40V,A42K,N43A,L44I)1,Zvar(Q9A,N11E,N28A,Q40V,A42K,N43A,L44I)1,Zvar(N11K,H18K,S33K,D37E,A42R,N43A,L44I, K50R,L51Y)1,Zvar(Q9A,N11K,H18K,S33K,D37E,A42R,N43A,L44I,K50R,L51Y)1, Zvar(N11K,H18K, D37E, A42R, N43A, L44I)1, Zvar(Q9A, N11K, H18K, D37E, A42R, N43A,L44I)1 and Zvar(Q9A, N11K, H18K, D37E, A42R, N43A, L44I, K50R)1 have animproved alkali stability compared to the parental structure Zvar1, usedas the reference. Further, the ligands B(Q9A,N11E,Q40V,A42K,N43A,L44I)1and C(Q9A,N11E,E43A)1 have an improved stability compared to theparental B and C domains, used as references.

TABLE 1 Monomeric ligands, evaluated by Biacore (0.5M NaOH). ReferenceCapacity Capacity capacity relative after 96-100 after 96-100 to LigandSequence cycles cycles reference Zvar(N11E, Q32A)1 SEQ ID 57% 55% 1.036NO 12 Zvar(N11E)1 SEQ ID 59% 55% 1.073 NO 13 Zvar(N11E, Q32E, Q40E)1 SEQID 52% 51% 1.020 NO 14 Zvar(N11E, Q32E, K50R)1 SEQ ID 53% 51% 1.039 NO15 Zvar(N11K)1 SEQ ID 62% 49% 1.270 NO 16 Zvar(N11Y)1 SEQ ID 55% 46%1.20 NO 38 Zvar(N11T)1 SEQ ID 50% 46% 1.09 NO 39 Zvar(N11F)1 SEQ ID 55%46% 1.20 NO 40 Zvar(N11L)1 SEQ ID 57% 47% 1.21 NO 41 Zvar(N11W)1 SEQ ID57% 47% 1.21 NO 42 Zvar(N11I)1 SEQ ID 57% 47% 1.21 NO 43 Zvar(N11M)1 SEQID 58% 46% 1.26 NO 44 Zvar(N11V)1 SEQ ID 56% 46% 1.22 NO 45 Zvar(N11A)1SEQ ID 58% 46% 1.26 NO 46 Zvar(N11H)1 SEQ ID 57% 46% 1.24 NO 47Zvar(N11R)1 SEQ ID 59% 46% 1.28 NO 48 Zvar(Q9A, N11E, N43A)1 SEQ ID 70%47% 1.49 NO 8 Zvar(Q9A, N11E, N28A, N43A)1 SEQ ID 68% 47% 1.45 NO 9Zvar(Q9A, N11E, Q40V, A42K, N43E, L44I)1 SEQ ID 67% 47% 1.43 NO 10Zvar(Q9A, N11E, Q40V, A42K, N43A, L44I)1 SEQ ID 66% 47% 1.40 NO 11Zvar(Q9A, N11E, N28A, Q40V, A42K, N43A, L44I)1 SEQ ID 65% 48% 1.35 NO 24Zvar(N11K, H18K, S33K, D37E, A42R, N43A, L44I, K50R, L51Y)1 SEQ ID 67%46% 1.46 NO 23 Zvar(Q9A, N11K, H18K, S33K, D37E, A42R, N43A, L44I, K50R,L51Y)1 SEQ ID 59% 46% 1.28 NO 25 Zvar(N11K, H18K, D37E, A42R, N43A,L44I)1 SEQ ID 59% 45% 1.31 NO 26 Zvar(Q9A, N11K, H18K, D37E, A42R, N43A,L44I)1 SEQ ID 63% 45% 1.40 NO 27 Zvar(Q9A, N11K, H18K, D37E, A42R, N43A,L44I, K50R)1 SEQ ID 67% 45% 1.49 NO 28 B(Q9A, N11E, Q40V, A42K, N43A,L44I)1 SEQ ID 39% 35% 1.11 NO 36 C(Q9A, N11E, E43A)1 SEQ ID 60% 49% 1.22NO 37

Example 2

The purified tetrameric and hexameric ligands listed in Table 2 wereimmobilized on Biacore CM5 sensor chips (GE Healthcare, Sweden), usingthe amine coupling kit of GE Healthcare (for carbodiimide coupling ofamines on the carboxymethyl groups on the chip) in an amount sufficientto give a signal strength of about 200-1500 RU in a Biacore instrument(GE Healthcare, Sweden) . To follow the IgG binding capacity of theimmobilized surface 1 mg/ml human polyclonal IgG (Gammanorm) was flowedover the chip and the signal strength (proportional to the amount ofbinding) was noted. The surface was then cleaned-in-place (CIP), i.e.flushed with 500 mM NaOH for 10 minutes at room temperature (22+/−2°C.). This was repeated for 300 cycles and the immobilized ligandalkaline stability was followed as the remaining IgG binding capacity(signal strength) after each cycle. The results are shown in Table 2 andin FIG. 2 and indicate that at least the ligands Zvar(Q9A,N11E,N43A)4,Zvar(Q9A,N11E,N28A,N43A)4, Zvar(Q9A,N11E,Q40V,A42K,N43E,L44I)4 andZvar(Q9A,N11E,Q40V,A42K,N43A,L44I)4,Zvar(Q9A,N11E,D37E,Q40V,A42K,N43A,L44I)4 andZvar(Q9A,N11E,D37E,Q40V,A42R,N43A,L44I)4 have an improved alkalistability compared to the parental structure Zvar4, which was used as areference. The hexameric ligand Zvar(Q9A,N11E,Q40V,A42K,N43A,L44I)6 alsohas improved alkali stability compared to the parental structure Zvar6,used as a reference.

TABLE 2 Tetrameric and hexameric ligands, evaluated by Biacore (0.5MNaOH). Capacity Capacity Capacity Remaining relative Remaining relativeRemaining relative SEQ capacity to ref. capacity to ref. capacity toref. ID 100 cycles 100 200 cycles 200 300 cycles 300 Ligand NO: (%)cycles (%) cycles (%) cycles Zvar4 21 67 1 36 1 16 1Zvar(Q9A,N11E,N43A)4 17 81 1.21 62 1.72 41 2.56 Zvar(Q9A,N11E,N28A,N 1880 1.19 62 1.72 42 2.62 43A)4 Zvar(Q9A,N11E,Q40V,A 19 84 1.25 65 1.81 483.00 42K,N43E,L44I)4 Zvar(Q9A,N11E,Q40V,A 20 90 1.34 74 2.06 57 3.5642K,N43A,L4404 Zvar(Q9A,N11E,N28A,Q 32 84 1.24 Not tested Not Not testedNot 40V,A42K,N43A,L44I)4 tested tested Zvar(Q9A,N11E,Q40V,A 33 87 1.30Not tested Not Not tested Not 42K,N43A,L4406 tested testedZvar(Q9A,N11E,D37E,Q 34 81 1.13 Not tested Not Not tested Not40V,A42K,N43A,L44I)4 tested tested Zvar(Q9A,N11E,D37E,Q 35 84 1.17 Nottested Not Not tested Not 40V,A42R,N43A,L44I)4 tested tested

Example 3

Example 2 was repeated with 100 CIP cycles of three ligands using 1 MNaOH instead of 500 mM as in Example 2. The results are shown in Table 3and show that all three ligands have an improved alkali stability alsoin 1M NaOH, compared to the parental structure Zvar4 which was used as areference.

TABLE 3 Tetrameric ligands, evaluated by Biacore (1M NaOH). RemainingCapacity capacity 100 relative to Ligand Sequence cycles (%) ref. 100cycles Zvar4 SEQ ID NO 21 27 1 Zvar(Q9A, N11E, N28A, SEQ ID NO 18 552.04 N43A)4 Zvar(Q9A, N11E, Q40V, SEQ ID NO 19 54 2.00 A42K, N43E,L44I)4 Zvar(Q9A, N11E, Q40V, SEQ ID NO 20 56 2.07 A42K, N43A, L44I)4

Example 4

The purified tetrameric ligands of Table 2 (all with an additionalN-terminal cysteine) were immobilized on agarose beads using the methodsdescribed below and assessed for capacity and stability. The results areshown in Table 4 and FIG. 3.

TABLE 4 Matrices with tetrametric ligands, evaluated in columns (0.5MNaOH). Remaining Capacity IgG Remaining retention Initial capacity IgGrelative IgG Qb10 capacity to ref. SEQ Ligand capacity after six 4 aftersix 4 after ID content Qb10 h cycles h cycles six 4 h Ligand NO. (mg/ml)(mg/ml) (mg/ml) (%) cycles Zvar4 21 7 52.5 36.5 60 1 Zvar4 21 12 61.143.4 71 1 Zvar(Q9A,N11E,N28A,N43A)4 18 7.0 49.1 44.1 90 1.50Zvar(Q9A,N11E,N28A,N43A)4 18 12.1 50.0 46.2 93 1.31Zvar(Q9A,N11E,Q40V,A42K,N43A,L44I)4 20 7.2 49.0 44.2 90 1.50Zvar(Q9A,N11E,Q40V,A42K,N43A,L44I)4 20 12.8 56.3 53.6 95 1.34Zvar(N11K,H18K,S33K,D37E,A42R,N43A, 30 9.7 56.3 52.0 92 1.53L44I,K5OR,L51Y)4 Zvar(Q9A,N11K,H18K,D37E,A42R)4 31 10.8 56.9 52.5 921.30

Activation

The base matrix used was rigid cross-linked agarose beads of 85micrometers (volume-weighted, d50V) median diameter, prepared accordingto the methods of U.S. Pat. No. 6,602,990 and with a pore sizecorresponding to an inverse gel filtration chromatography Kay value of0.70 for dextran of Mw 110 kDa, according to the methods described inGel Filtration Principles and Methods, Pharmacia LKB Biotechnology 1991,pp 6-13.

25 mL (g) of drained base matrix, 10.0 mL distilled water and 2.02 gNaOH (s) was mixed in a 100 mL flask with mechanical stirring for 10 minat 25° C. 4.0 mL of epichlorohydrin was added and the reactionprogressed for 2 hours. The activated gel was washed with 10 gelsediment volumes (GV) of water.

Coupling

To 20 mL of ligand solution (50 mg/mL) in a 50 ml Falcon tube, 169 mgNaHCO₃, 21 mg Na₂CO₃, 175 mg NaCl and 7 mg EDTA, was added. The Falcontube was placed on a roller table for 5-10 min, and then 77 mg of DTEwas added. Reduction proceeded for >45 min. The ligand solution was thendesalted on a PD10 column packed with Sephadex G-25. The ligand contentin the desalted solution was determined by measuring the 276 nm UVabsorption.

The activated gel was washed with 3-5 GV {0.1 M phosphate/1 mM EDTA pH8.6} and the ligand was then coupled according to the method describedin U.S. Pat. No. 6,399,750. All buffers used in the experiments had beendegassed by nitrogen gas for at least 5-10 min. The ligand content ofthe gels could be controlled by varying the amount and concentration ofthe ligand solution.

After immobilization the gels were washed 3×GV with distilled water. Thegels+1 GV {0.1 M phosphate/1 mM EDTA/10% thioglycerol pH 8.6} was mixedand the tubes were left in a shaking table at room temperatureovernight. The gels were then washed alternately with 3×GV {0.1 MTRIS/0.15 M NaCl pH 8.6} and 0.5 M HAc and then 8-10×GV with distilledwater. Gel samples were sent to an external laboratory for amino acidanalysis and the ligand content (mg/ml gel) was calculated from thetotal amino acid content.

Protein

Gammanorm 165 mg/ml (Octapharma), diluted to 2 mg/ml in Equilibrationbuffer.

Equilibration Buffer

PBS Phosphate buffer 10 mM+0.14 M NaCl+0.0027 M KCl, pH 7.4 (Medicago)

Adsorption Buffer

PBS Phosphate buffer 10 mM+0.14 M NaCl+0.0027 M KCl, pH 7.4 (Medicago)

Elution Buffers

100 mM acetate pH 2.9

Dynamic Binding Capacity

2 ml of resin was packed in TRICORN™ 5 100 columns. The breakthroughcapacity was determined with an ÄKTAExplorer 10 system at a residencetime of 6 minutes (0.33 ml/min flow rate). Equilibration buffer was runthrough the bypass column until a stable baseline was obtained. This wasdone prior to auto zeroing. Sample was applied to the column until a100% UV signal was obtained. Then, equilibration buffer was appliedagain until a stable baseline was obtained.

Sample was loaded onto the column until a UV signal of 85% of maximumabsorbance was reached. The column was then washed with 5 column volumes(CV) equilibration buffer at flow rate 0.5 ml/min. The protein waseluted with 5 CV elution buffer at a flow rate of 0.5 ml/min. Then thecolumn was cleaned with 0.5M NaOH at flow rate 0.2 ml/min andre-equilibrated with equilibration buffer.

For calculation of breakthrough capacity at 10%, the equation below wasused. That is the amount of IgG that is loaded onto the column until theconcentration of IgG in the column effluent is 10% of the IgGconcentration in the feed.

$q_{10\%} = {\frac{C_{0}}{V_{C}}\left\lbrack {V_{app} - V_{sys} - {\int_{V_{sys}}^{V_{app}}{\frac{{A(V)} - A_{sub}}{A_{100\%} - A_{sub}}*{dv}}}} \right\rbrack}$

A₁₀₀%=100% UV signal;

A_(sub)=absorbance contribution from non-binding IgG subclass;

A(V)=absorbance at a given applied volume;

V_(c)=column volume;

V_(app)=volume applied until 10% breakthrough;

V_(sys)=system dead volume;

C₀=feed concentration.

The dynamic binding capacity (DBC) at 10% breakthrough was calculated.The dynamic binding capacity (DBC) was calculated for 10 and 80%breakthrough.

CIP −0.5 M NaOH

The 10% breakthrough DBC (Qb10) was determined both before and afterrepeated exposures to alkaline cleaning solutions. Each cycle included aCIP step with 0.5 M NaOH pumped through the column at a rate of 0.5/minfor 20 min, after which the column was left standing for 4 h. Theexposure took place at room temperature (22+/−2° C.). After thisincubation, the column was washed with equilibration buffer for 20 minat a flow rate of 0.5 ml/min. Table 4 shows the remaining capacity aftersix 4 h cycles (i.e. 24 h cumulative exposure time to 0.5 M NaOH), bothin absolute numbers and relative to the initial capacity.

Example 5

Example 4 was repeated with the tetrameric ligands shown in Table 5, butwith 1.0 M NaOH used in the CIP steps instead of 0.5 M. The results areshown in Table 5 and in FIG. 4.

TABLE 5 Matrices with tetrametric ligands, evaluated in columns - 1.0MNaOH. Remaining Capacity IgG Remaining retention Initial capacity IgGrelative IgG Qb10 capacity to ref. SEQ Ligand capacity after six 4 aftersix 4 after ID content Qb10 h cycles h cycles six 4 h Ligand NO. (mg/ml)(mg/ml) (mg/ml) (%) cycles Zvar4 21 12 60.1 33.5 56 1Zvar(Q9A,N11E,Q40V,A42K,N43A,L44I)4 20 12.8 60.3 56.0 93 1.67Zvar(N11K,H18K,S33K,D37E,A42R,N43A, 30 9.7 62.1 48.1 77 1.44L44I,K50R,L51Y)4

This written description uses examples to disclose the invention,including the best mode, and also to enable any person skilled in theart to practice the invention, including making and using any devices orsystems and performing any incorporated methods. The patentable scope ofthe invention is defined by the claims, and may include other examplesthat occur to those skilled in the art. Such other examples are intendedto be within the scope of the claims if they have structural elementsthat do not differ from the literal language of the claims, or if theyinclude equivalent structural elements with insubstantial differencesfrom the literal languages of the claims. All patents and patentapplications mentioned in the text are hereby incorporated by referencein their entireties, as if they were individually incorporated.

1-49. (canceled)
 50. A separation matrix comprising: an Fc-bindingpolypeptide, wherein the polypeptide comprises: a) a mutant of anFc-binding domain of Staphylococcus Protein A (SpA) having the aminoacid sequence of SEQ ID NO: 52, wherein the amino acid residue at theposition corresponding to position 5 in SEQ ID NO: 52 is alanine, or avariant of the mutant having at least 90% identity thereto; and b) alinker comprising 5-10 amino acids coupled to the mutant, wherein linkeris free of proline, asparagine, and glutamine; and a solid supportcomprising crosslinked agarose, wherein the Fc-binding polypeptide iscoupled to the solid support.
 51. The separation matrix of claim 50,wherein the IgG capacity of the matrix after 24 h incubation in 0.5 MNaOH at 22+/−2° C. is at least 95% of the IgG capacity before theincubation.
 52. The separation matrix of claim 50, wherein thepolypeptide coupling to the solid support comprises a bridge couplingbetween at least one coupling amino acid on the polypeptide and anelectrophilic group on the support.
 53. The separation matrix of claim52, wherein the bridge coupling comprises a thioether bond.
 54. Theseparation matrix of claim 52, wherein the coupling amino acid isselected from one or more of cysteine, lysine, or histidine.
 55. Theseparation matrix of claim 52, wherein the coupling is multipointcoupling through two lysines.
 56. The separation matrix of claim 50,wherein a plurality of Fc binding polypeptides have been coupled to thecrosslinked agarose.
 57. A separation matrix comprising: a multimercomprising a plurality of Fc-binding polypeptides, wherein eachpolypeptide comprises: a) a mutant of an Fc-binding domain ofStaphylococcus Protein A (SpA) having the amino acid sequence of SEQ IDNO: 52, wherein the amino acid residue at the position corresponding toposition 5 in SEQ ID NO: 52 is alanine, or a variant of the mutanthaving at least 90% identity thereto; and b) a linker comprising 5-10amino acids coupled to the mutant, wherein linker is free of proline,asparagine, and glutamine; and a solid support comprising crosslinkedagarose, wherein the multimer is coupled to the solid support.
 58. Theseparation matrix of claim 57, which is a dimer, trimer, tetramer,pentamer, hexamer, heptamer, octamer, or nonamer.
 59. The separationmatrix of claim 57, which is a pentamer.
 60. The separation matrix ofclaim 57, wherein the IgG capacity of the matrix after 24 h incubationin 0.5 M NaOH at 22+/−2° C. is at least 95% of the IgG capacity beforethe incubation.
 61. The separation matrix of claim 57, wherein themultimer coupling to the solid support comprises a bridge couplingbetween at least one coupling amino acid on a polypeptide of themultimer and an electrophilic group on the support.
 62. The separationmatrix of claim 61, wherein the bridge coupling comprises a thioetherbond.
 63. The separation matrix of claim 61, wherein the coupling aminoacid is selected from one or more of cysteine, lysine, or histidine. 64.The separation matrix of claim 63, wherein the coupling is multipointcoupling through two lysines.
 65. The separation matrix of claim 57,wherein a plurality of multimers have been coupled to the crosslinkedagarose.